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Minor proteins, mobile arms and membrane–capsid interactions in the bacteriophage PRD1 capsid

Nature Structural Biology volume 9, pages 756–763 (2002)Cite this article

Abstract

Bacteriophage PRD1 shares many structural and functional similarities with adenovirus. A major difference is the PRD1 internal membrane, which acts in concert with vertex proteins to translocate the phage genome into the host. Multiresolution models of the PRD1 capsid, together with genetic analyses, provide fine details of the molecular interactions associated with particle stability and membrane dynamics. The N- and C-termini of the major coat protein (P3), which are required for capsid assembly, act as conformational switches bridging capsid to membrane and linking P3 trimers. Electrostatic P3–membrane interactions increase virion stability upon DNA packaging. Newly revealed proteins suggest how the metastable vertex works and how the capsid edges are stabilized.

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Figure 1: Central sections of the PRD1 cryo-EM reconstructions, filtered quasi-atomic models and difference maps, as indicated.
Figure 2: Location of difference peaks in the PRD1 capsid.
Figure 3: Vertex complex.
Figure 4: Capsid–membrane contacts.
Figure 5: C-terminal network in the PRD1 facet.
Figure 6: Protein P30.
Figure 7: Stabilizing interactions in the capsid.

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Protein Data Bank

References

  1. Olsen, R.H., Siak, J.-S. & Gray, R.H. Characteristics of PRD1, a plasmid-dependent broad host range DNA bacteriophage. J. Virol. 14, 689–699 (1974).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Bamford, D.H., Caldentey, J. & Bamford, J.K.H. Bacteriophage PRD1: a broad host range dsDNA tectivirus with an internal membrane. Adv. Virus Res. 45, 281–319 (1995).

    Article  CAS  Google Scholar 

  3. San Martín, C. et al. Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1, and shows key capsid and membrane interactions. Structure 9, 917–930 (2001).

    Article  Google Scholar 

  4. Butcher, S.J., Bamford, D.H. & Fuller, S.D. DNA packaging orders the membrane of bacteriophage PRD1. EMBO J. 14, 6078–6086 (1995).

    Article  CAS  Google Scholar 

  5. Bamford, J.K.H. et al. Diffraction quality crystals of PRD1, a 66 MDa dsDNA virus with an internal membrane. J. Struct. Biol. in the press (2002).

  6. Caldentey, J., Blanco, L., Bamford, D.H. & Salas, M. In vitro replication of bacteriophage PRD1 DNA. Characterization of the protein-primed initiation site. Nucleic Acids Res. 21, 3725–3730 (1993).

    Article  CAS  Google Scholar 

  7. King, A.J. & van der Vliet, P.C. A precursor terminal protein-trinucleotide intermediate during initiation of adenovirus DNA replication: regeneration of molecular ends in vitro by a jumping back mechanism. EMBO J. 13, 5786–5792 (1994).

    Article  CAS  Google Scholar 

  8. Stewart, P.L., Burnett, R.M., Cyrklaff, M. & Fuller, S.D. Image reconstruction reveals the complex molecular organization of adenovirus. Cell 67, 145–154 (1991).

    Article  CAS  Google Scholar 

  9. Rydman, P.S. et al. Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex. J. Mol. Biol. 291, 575–587 (1999).

    Article  CAS  Google Scholar 

  10. Benson, S.D., Bamford, J.K.H., Bamford, D.H. & Burnett, R.M. Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98, 825–833 (1999).

    Article  CAS  Google Scholar 

  11. Rux, J.J. & Burnett, R.M. Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon. Mol. Ther. 1, 18–30 (2000).

    Article  CAS  Google Scholar 

  12. Tuma, R., Bamford, J.K.H., Bamford, D.H., Russell, M.P. & Thomas, G.J. Jr Structure, interactions and dynamics of PRD1 virus I. Coupling of subunit folding and capsid assembly. J. Mol. Biol. 257, 87–101 (1996).

    Article  CAS  Google Scholar 

  13. Xu, L., Butcher, S.J., Benson, S.D., Bamford, D.H. & Burnett, R.M. Crystallization and preliminary X-ray analysis of receptor-binding protein P2 of bacteriophage PRD1. J. Struct. Biol. 131, 159–163 (2000).

    Article  CAS  Google Scholar 

  14. Sokolova, A. et al. Solution structure of bacteriophage PRD1 vertex complex. J. Biol. Chem. 276, 46187–46195 (2001).

    Article  CAS  Google Scholar 

  15. Benson, S.D., Bamford, J.K.H., Bamford, D.H. & Burnett, R.M. The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 Å resolution. Acta Crystallogr. D 58, 39–59 (2002).

    Article  Google Scholar 

  16. Stewart, P.L., Fuller, S.D. & Burnett, R.M. Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy. EMBO J. 12, 2589–2599 (1993).

    Article  CAS  Google Scholar 

  17. Mindich, L., Bamford, D., McGraw, T. & Mackenzie, G. Assembly of bacteriophage PRD1: particle formation with wild-type and mutant viruses. J. Virol. 44, 1021–1030 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Mindich, L., Bamford, D., Goldthwaite, C., Laverty, M. & Mackenzie, G. Isolation of nonsense mutants of lipid-containing bacteriophage PRD1. J. Virol. 44, 1013–1020 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Luo, C., Butcher, S. & Bamford, D.H. Isolation of a phospholipid-free protein shell of bacteriophage PRD1, an Escherichia coli virus with an internal membrane. Virology 194, 564–569 (1993).

    Article  CAS  Google Scholar 

  20. Rydman, P.S., Bamford, J.K.H. & Bamford, D.H. A minor capsid protein P30 is essential for bacteriophage PRD1 capsid assembly. J. Mol. Biol. 313, 785–795 (2001).

    Article  CAS  Google Scholar 

  21. Bamford, J.K.H. & Bamford, D.H. A new mutant class, made by targeted mutagenesis, of phage PRD1 reveals that protein P5 connects the receptor binding protein to the vertex. J. Virol. 74, 7781–7786 (2000).

    Article  CAS  Google Scholar 

  22. Grahn, A.M., Caldentey, J., Bamford, J.K.H. & Bamford, D.H. Stable packaging of phage PRD1 DNA requires adsorption protein P2, which binds to the IncP plasmid-encoded conjugative transfer complex. J. Bacteriol. 181, 6689–6696 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Grahn, A.M., Daugelavicius, R. & Bamford, D.H. The small viral membrane-associated protein P32 is involved in bacteriophage PRD1 DNA entry. J. Virol. 76, 4866–4872 (2002).

    Article  CAS  Google Scholar 

  24. Davis, T.N., Muller, E.D. & Cronan, J.E. Jr The virion of the lipid-containing bacteriophage PR4. Virology 120, 287–306 (1982).

    Article  CAS  Google Scholar 

  25. Bamford, J.K.H. et al. Genome organization of membrane-containing bacteriophage PRD1. Virology 183, 658–676. (1991).

    Article  CAS  Google Scholar 

  26. Burnett, R.M. in Structural Biology of Viruses (eds Chiu, W., Burnett, R.M. & Garcea, R.L.) 209–238 (Oxford University Press, New York; 1997).

    Google Scholar 

  27. Caldentey, J., Tuma, R. & Bamford, D.H. Assembly of bacteriophage PRD1 spike complex: role of the multidomain protein P5. Biochemistry 39, 10566–10573 (2000).

    Article  CAS  Google Scholar 

  28. Olson, A.J., Bricogne, G. & Harrison, S.C. Structure of tomato bushy stunt virus IV. The virus particle at 2.9 Å resolution. J. Mol. Biol. 171, 61–93 (1983).

    Article  CAS  Google Scholar 

  29. Stehle, T., Gamblin, S.J., Yan, Y. & Harrison, S.C. The structure of simian virus 40 refined at 3.1 Å resolution. Structure 4, 165–182 (1996).

    Article  CAS  Google Scholar 

  30. Fisher, A.J. & Johnson, J.E. Ordered duplex RNA controls capsid architecture in an icosahedral animal virus. Nature 361, 176–179 (1993).

    Article  CAS  Google Scholar 

  31. Bamford, D.H., Burnett, R.M. & Stuart, D.I. Evolution of viral structure. Theor. Popul. Biol. 61, 461–470 (2002).

    Article  Google Scholar 

  32. Strauss, J.H. & Strauss, E.G. Virus evolution: how does an enveloped virus make a regular structure? Cell 105, 5–8 (2001).

    Article  CAS  Google Scholar 

  33. Sambrook, J. & Russell, D.W. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor; 2001).

    Google Scholar 

  34. Campbell, J.L., Richardson, C.C. & Studier, F.W. Genetic recombination and complementation between bacteriophage T7 and cloned fragments of T7 DNA. Proc. Natl. Acad. Sci. USA 75, 2276–2280 (1978).

    Article  CAS  Google Scholar 

  35. Bamford, J.K.H. & Bamford, D.H. Capsomer proteins of bacteriophage PRD1, a bacterial virus with a membrane. Virology 177, 445–451 (1990).

    Article  CAS  Google Scholar 

  36. Mindich, L. & McGraw, T. Molecular cloning of bacteriophage PRD1 genomic fragments. Mol. Gen. Genet. 190, 233–236 (1983).

    Article  CAS  Google Scholar 

  37. Hänninen, A.-L., Bamford, D.H. & Bamford, J.K.H. Probing phage PRD1-specific proteins with monoclonal and polyclonal antibodies. Virology 227, 198–206 (1997).

    Article  Google Scholar 

  38. Walin, L., Tuma, R., Thomas, G.J. Jr & Bamford, D.H. Purification of viruses and macromolecular assemblies for structural investigations using a novel ion exchange method. Virology 201, 1–7 (1994).

    Article  CAS  Google Scholar 

  39. Harauz, G. & van Heel, M. Exact filters for general geometry three-dimensional reconstruction. Optik 73, 146–156 (1986).

    Google Scholar 

  40. Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996).

    Article  CAS  Google Scholar 

  41. Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. in International Tables for Crystallography Vol. F. (eds Rossmann, M.G. & Arnold, E.) Ch. 17.1, 353–356 (Kluwer Academic Publishers, Dordrecht; 2001).

    Google Scholar 

  42. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  43. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  44. Esnouf, R.M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr. D 55, 938–940 (1999).

    Article  CAS  Google Scholar 

  45. Merritt, E.A. & Bacon, D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505–524 (1997).

    Article  CAS  Google Scholar 

  46. Nicholls, A., Sharp, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296 (1991).

    Article  CAS  Google Scholar 

  47. Bartolomé, B., Jubete, Y., Martínez, E. & de la Cruz, F. Construction and properties of a family of pACYC184-derived cloning vectors compatible with pBR322 and its derivatives. Gene 102, 75–78 (1991).

    Article  Google Scholar 

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Acknowledgements

We are thankful to S.D. Benson, L. Xu, J.J. Rux, F. de Haas and R. Tuma for helpful discussions and suggestions; P. Laurinmäki and the Electron Microscopy unit of the Institute of Biotechnology for expert electron microscopy; and R. Marabini and E. Garduño for help with OpenDX. C.S.M. is partially supported by a PNFPI Fellowship from the Spanish Ministerio de Educación, Cultura y Deporte. J.T.H. is supported by the National Graduate School in Informational and Structural Biology. J.K.H.B. and S.J.B. are Academy of Finland Senior Researchers. S.D.F. is a Wellcome Trust Principal Research Fellow. This collaborative work was supported by the Human Frontiers Science Program (D.H.B. and R.M.B.), the Academy of Finland Centre of Excellence Programme (2000–2005) (D.H.B.), and the National Science Foundation, the National Institutes of Health, the Wistar Institute Cancer Center and the Fannie E. Rippel Foundation (R.M.B.).

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Authors and Affiliations

  1. The Wistar Institute, 3601 Spruce Street, Philadelphia, 19104, Pennsylvania, USA

    Carmen San Martín & Roger M. Burnett

  2. Department of Biosciences and Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56 (Viikinkaari 5), Helsinki, 00014, Finland

    Juha T. Huiskonen, Jaana K. H. Bamford, Sarah J. Butcher & Dennis H. Bamford

  3. The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, The Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Headington, OX3 7BN, Oxford, UK

    Stephen D. Fuller

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Correspondence to Roger M. Burnett.

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San Martín, C., Huiskonen, J., Bamford, J. et al. Minor proteins, mobile arms and membrane–capsid interactions in the bacteriophage PRD1 capsid. Nat Struct Mol Biol 9, 756–763 (2002). https://doi.org/10.1038/nsb837

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